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TileDB example - #136
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tien-tong wants to merge 2 commits into
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TileDB example#136tien-tong wants to merge 2 commits into
tien-tong wants to merge 2 commits into
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ModelArray() can open a TileDB store from a URI once the TileDB context is configured (e.g. a public s3:// bucket), but ModelArraySummary() stopped with "File not found": it checked file.exists() and listed subdirectories with local-only calls, which fail for any URI (a file:// URI fails the same way). Resolve the storage backend first; for TileDB use TileDB's own VFS (tiledb_vfs_is_dir / tiledb_vfs_ls) to test the store and list scalars/ and results/, so local paths and URIs share one code path. file.exists() now runs only in the HDF5 branch. New tests cover a file:// summary (equal to the local summary), group internals/stray files being ignored, a missing store, and the HDF5 path still erroring on file://. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
A parameterized report (inst/examples/rbc-s3-tiledb/) that reads the RBC FreeSurferPost TileDB store straight from its public S3 bucket -- without downloading the 553 GB dataset -- and fits vertex-wise GAMs of cortical thickness on age in two Glasser parcels at opposite ends of the sensorimotor-association axis (area 3b and area 46). It harmonizes the nine scanning sites with CovBat, checks the result against the known maturational ordering (3b early, 46 late), and exports CIFTI maps for Connectome Workbench. Ships vendored Glasser-164k parcel labels, the Sydnor et al. 2021 S-A axis ranks, and S-A brain images in that paper's Figure 2A colour scheme (all with provenance scripts). Adds the vignette "Cloud TileDB: RBC Cortical Thickness from S3" (pkgdown Case Studies) with a Binder badge and a binder/ environment so it can be run in the browser, rewrites the covfam case study in modelling.Rmd to the real ComBatFamily API, and notes remote-URI support in installations.Rmd. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Codecov Report❌ Patch coverage is
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## main #136 +/- ##
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Coverage 91.66% 91.66%
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Files 6 6
Lines 2542 2543 +1
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+ Hits 2330 2331 +1
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